def substackTrajectory(trajectory, selection):
# Get the current positions
crt_positions = trajectory.positions
# Make the selection
crt_positions = crt_positions[crt_positions['frame'].isin(selection)]
# Remap the frame indices
old_frames = crt_positions['frame'].unique()
new_frames = np.arange(old_frames.shape[0])
convert_dict = dict(zip(old_frames, new_frames))
# Convert the values
new_frame_positions = np.copy(crt_positions['frame'].to_numpy())
for key in convert_dict.keys():
new_frame_positions[new_frame_positions == key] = convert_dict[key]
# Replace the trajectory
new_positions = crt_positions.copy()
new_positions['frame'] = new_frame_positions
# Generate the new manager
new_trajectory = startManager(new_positions)
return new_trajectory
def getTrajectory(self, trj):
# Save the trajectory in the class
self.image_class.trajectory = startManager(trj)
# Close the progress bar window
self.close()
self.scheduler.stackProcessed()
def generateTrajectory(positions):
# Format the pandas dataframe
positions = positions[['y', 'x']].copy()
positions['frame'] = [0] * len(positions['x'])
positions['particle'] = np.arange(len(positions['x']))
positions.reset_index(drop=True, inplace=True)
# Initialise the manager
trajectory = startManager(positions)
return trajectory
def callLoadTrajectory(self):
# Check if a tab is open
if len(self.parent.imageTabDisplay.displayedTabs) > 0:
# Open the load file browser
trajectoryFile, _ = qtw.QFileDialog.getOpenFileName(
self.parent, "Load Trajectory File...", "",
"Hierarchical Data (*.xml);;All Files (*)")
# Retrieve the current tab ID
tab_id = self.parent.imageTabDisplay.currentIndex()
# Load the trajectory in the session
if trajectoryFile != "":
self.parent.imageTabDisplay.displayedTabs[
tab_id].image_class.trajectory = startManager(
trajectoryFile)
# Check that the length matches
n_traj = len(
self.parent.imageTabDisplay.displayedTabs[tab_id].
image_class.trajectory.positions['frame'].unique())
n_frames = self.parent.imageTabDisplay.displayedTabs[
tab_id].image_class.n_frames
# Display a warning
if n_traj != n_frames:
warningMessage(
"Different Number of Frames",
"The number of frames in the image stack and the number of frames in the trajectory do not match. This could lead to issues for displaying the positions of the particles."
)
# Open the trajectory side bar
self.callTrajectoryManagerDock()
# Refresh the display
self.parent.imageTabDisplay.displayedTabs[
tab_id].refreshPathList()
self.parent.imageTabDisplay.displayedTabs[tab_id].displayImage(
)
else:
errorMessageNoImage()
def processTrajectory(self):
_proceed = True
# Load the selected trajectory - from file
if self.fromFileButton.isChecked(
) and self.loaded_trajectory is not None:
self.trajectory = startManager(self.loaded_trajectory)
# Load the selected trajectory - from image tab
elif self.fromImageButton.isChecked():
tab_id = self.parent.imageTabDisplay.currentIndex()
self.trajectory = self.parent.imageTabDisplay.displayedTabs[
tab_id].image_class.trajectory
else:
_proceed = False
# Process the loaded trajectory
if _proceed:
# Retrieve the scale
self.space_scale = float(self.spaceScaleEntry.text())
self.frame_rate = float(self.timeScaleEntry.text())
self.space_unit = self.spaceUnitEntry.text()
# Comvert the scale
micron_per_pixel = getSpaceScale(self.space_scale, self.space_unit)
# Get the list of paths
self.path_list = list(self.trajectory.listTracks())
# Extract the MSDs
self.lagtime = []
self.msd = []
# Get the combined MSD
crt_lagtime, crt_msd = getMSD(self.trajectory.positions,
micron_per_pixel, self.frame_rate)
self.lagtime.append(crt_lagtime)
self.msd.append(crt_msd)
# Get the individual MSDs
crt_lagtime, all_msd = getMSD(self.trajectory.positions,
micron_per_pixel,
self.frame_rate,
path_id=self.path_list)
for i in range(all_msd.shape[1]):
self.lagtime.append(crt_lagtime)
self.msd.append(all_msd[:, i])
# Get all the diffusivity
self.fits, self.diffusivity, self.diff_err = getDiffusivity(
self.lagtime, self.msd)
# Update the display
self.path_list.insert(0, 'All')
self.pathSelectionEntry.replaceList(
[str(x) for x in self.path_list])
# Update the graph
self.updateGraph()
self.saveButton.setEnabled(True)